Baobab LIMS is an open-source laboratory information management system. This software solution
focusses on quality management of the life cycle of biological specimens and their associated
metadata. The evolution of Baobab LIMS has included the development and implementation of a
viral module, separated from the classical biospecimen module in the LIMS. This viral module has
incorporated numerous fields from the PHA4GE SARS-CoV-2 contextual metadata template (which
can be found here), in order to ensure that data collection associated with samples for viral
workflows is extensive and standardized. The latest development combines ease of configuration
with future-proofing the module by incorporating hard-coded options, as well as configurable
content types, with an importer for the latter, already populated with recommended vocabularies
from the metadata standard, available for end-users. Collection of biospecimens for viral workflows
can be performed via an excel importer, to facilitate higher throughput. In addition, the Baobab
LIMS development team have included the Viral Genome Analysis module, which facilitates high
throughput analysis of samples for extracting genomic material, aliquoting the genomic material,
quantifying the genomic material, viral load determination via qPCR and sequence library
preparation with a library ID which can be used to link biospecimen QC with sequencing and/or
bioinformatics QC. The categories in the Viral Genome Analysis can be used all together, or in
combinations, depending on capacities of individual users.
combinations, depending on end-user workflow and capacity
module
A Baobab LIMS hands-on virtual training was hosted in partnership with the Africa CDC, on the 10 th
and 11 th of August. Fifteen participants from various laboratories on the continent were invited to
attend the training, with the first session demonstrating the overall capacity of Baobab LIMS, and
the second session with a focus on the newly created viral module. The Baobab LIMS team would
like to thank members from the Africa-CDC who assisted in facilitating the training, as well as the
participants who joined the training event.
In other news, Baobab LIMS was pitched at the Virtual Start-up Sprint, a collaborative course
between the University of the Western Cape and Mashauri. The pitch competition was included 5
entrepreneurs and was judged by a panel of experts. Baobab LIMS won the first prize of seed
funding, and the team opted to pay it forward by sharing the prize money with the second runner-
up.
Resources for Baobab LIMS are available here, and if you have any questions, lease contact us by
email to help@baobablims.org.